<!DOCTYPE html>
<html lang="en">
<head>
<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
<meta charset="utf-8">
<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
<title>Chapter 8 Sigflow pipeline | Extract, Analyze and Visualize Mutational Signatures with Sigminer</title>
<meta name="author" content="Shixiang Wang, PhD (Sun Yat-sen University Cancer Center)">
<meta name="author" content="Xue-Song Liu, PhD (ShanghaiTech University)">
<meta name="description" content="Sigflow provides useful mutational signature analysis workflows based on R package sigminer. It can auto-extract mutational signatures, fit mutation data to COSMIC reference signatures...">
<meta name="generator" content="bookdown 0.28 with bs4_book()">
<meta property="og:title" content="Chapter 8 Sigflow pipeline | Extract, Analyze and Visualize Mutational Signatures with Sigminer">
<meta property="og:type" content="book">
<meta property="og:description" content="Sigflow provides useful mutational signature analysis workflows based on R package sigminer. It can auto-extract mutational signatures, fit mutation data to COSMIC reference signatures...">
<meta name="twitter:card" content="summary">
<meta name="twitter:title" content="Chapter 8 Sigflow pipeline | Extract, Analyze and Visualize Mutational Signatures with Sigminer">
<meta name="twitter:description" content="Sigflow provides useful mutational signature analysis workflows based on R package sigminer. It can auto-extract mutational signatures, fit mutation data to COSMIC reference signatures...">
<!-- JS --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://kit.fontawesome.com/6ecbd6c532.js" crossorigin="anonymous"></script><script src="libs/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
<link href="libs/bootstrap-4.6.0/bootstrap.min.css" rel="stylesheet">
<script src="libs/bootstrap-4.6.0/bootstrap.bundle.min.js"></script><script src="libs/bs3compat-0.4.0/transition.js"></script><script src="libs/bs3compat-0.4.0/tabs.js"></script><script src="libs/bs3compat-0.4.0/bs3compat.js"></script><link href="libs/bs4_book-1.0.0/bs4_book.css" rel="stylesheet">
<script src="libs/bs4_book-1.0.0/bs4_book.js"></script><script src="libs/htmlwidgets-1.5.4/htmlwidgets.js"></script><link href="libs/datatables-css-0.0.0/datatables-crosstalk.css" rel="stylesheet">
<script src="libs/datatables-binding-0.24/datatables.js"></script><link href="libs/dt-core-1.11.3/css/jquery.dataTables.min.css" rel="stylesheet">
<link href="libs/dt-core-1.11.3/css/jquery.dataTables.extra.css" rel="stylesheet">
<script src="libs/dt-core-1.11.3/js/jquery.dataTables.min.js"></script><link href="libs/crosstalk-1.2.0/css/crosstalk.min.css" rel="stylesheet">
<script src="libs/crosstalk-1.2.0/js/crosstalk.min.js"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- CSS --><style type="text/css">
    
    div.hanging-indent{margin-left: 1.5em; text-indent: -1.5em;}
  </style>
<style type="text/css">
    /* Used with Pandoc 2.11+ new --citeproc when CSL is used */
    div.csl-bib-body { }
    div.csl-entry {
      clear: both;
        }
    .hanging div.csl-entry {
      margin-left:2em;
      text-indent:-2em;
    }
    div.csl-left-margin {
      min-width:2em;
      float:left;
    }
    div.csl-right-inline {
      margin-left:2em;
      padding-left:1em;
    }
    div.csl-indent {
      margin-left: 2em;
    }
  </style>
</head>
<body data-spy="scroll" data-target="#toc">

<div class="container-fluid">
<div class="row">
  <header class="col-sm-12 col-lg-3 sidebar sidebar-book"><a class="sr-only sr-only-focusable" href="#content">Skip to main content</a>

    <div class="d-flex align-items-start justify-content-between">
      <h1>
        <a href="index.html" title="">Extract, Analyze and Visualize Mutational Signatures with Sigminer</a>
      </h1>
      <button class="btn btn-outline-primary d-lg-none ml-2 mt-1" type="button" data-toggle="collapse" data-target="#main-nav" aria-expanded="true" aria-controls="main-nav"><i class="fas fa-bars"></i><span class="sr-only">Show table of contents</span></button>
    </div>

    <div id="main-nav" class="collapse-lg">
      <form role="search">
        <input id="search" class="form-control" type="search" placeholder="Search" aria-label="Search">
</form>

      <nav aria-label="Table of contents"><h2>Table of contents</h2>
        <ul class="book-toc list-unstyled">
<li><a class="" href="index.html">📖 Introduction</a></li>
<li class="book-part">Part I: Background and Prerequisite</li>
<li><a class="" href="mutsig-intro.html"><span class="header-section-number">1</span> Mutational signatures</a></li>
<li><a class="" href="prerequisite.html"><span class="header-section-number">2</span> Package prerequisite and installation</a></li>
<li class="book-part">Part II: Workflows</li>
<li><a class="" href="basic-workflow.html"><span class="header-section-number">3</span> Mutational signature analysis basics</a></li>
<li><a class="" href="analysis-supps.html"><span class="header-section-number">4</span> Other signature types</a></li>
<li><a class="" href="target-vis.html"><span class="header-section-number">5</span> Target visualization</a></li>
<li class="book-part">Part III: Miscellaneous topics</li>
<li><a class="" href="universal-analysis.html"><span class="header-section-number">6</span> Universal analysis</a></li>
<li><a class="" href="subtype-prediction.html"><span class="header-section-number">7</span> Subtype prediction</a></li>
<li><a class="active" href="sigflow.html"><span class="header-section-number">8</span> Sigflow pipeline</a></li>
<li><a class="" href="datasets.html"><span class="header-section-number">9</span> Datasets</a></li>
<li><a class="" href="convert.html"><span class="header-section-number">10</span> SBS signature conversion</a></li>
<li class="book-part">Appendix</li>
<li><a class="" href="references.html">References</a></li>
</ul>

        <div class="book-extra">
          
        </div>
      </nav>
</div>
  </header><main class="col-sm-12 col-md-9 col-lg-7" id="content"><div id="sigflow" class="section level1" number="8">
<h1>
<span class="header-section-number">8</span> Sigflow pipeline<a class="anchor" aria-label="anchor" href="#sigflow"><i class="fas fa-link"></i></a>
</h1>
<p><a href="https://github.com/ShixiangWang/sigflow"><strong>Sigflow</strong></a> provides useful mutational signature analysis workflows based on R package <strong>sigminer</strong>. It can auto-extract mutational signatures, fit mutation data to COSMIC reference signatures (SBS/DBS/INDEL) and run bootstrapping analysis for signature fitting.</p>
<p>For full documentation, please read Sigflow <a href="https://github.com/ShixiangWang/sigflow"><em>README</em></a>.</p>
<div id="cancer-type-specific-signature-index-database" class="section level2" number="8.1">
<h2>
<span class="header-section-number">8.1</span> Cancer type specific signature index database<a class="anchor" aria-label="anchor" href="#cancer-type-specific-signature-index-database"><i class="fas fa-link"></i></a>
</h2>
<p>Signature fitting analysis may befit from directly specifying known signatures identified in a cancer type. We collect such information and provide the following data tables.</p>
<div class="sourceCode" id="cb88"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="va">db1</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.file.html">system.file</a></span><span class="op">(</span><span class="st">"extdata"</span>, <span class="st">"cosmic2_record_by_cancer.rds"</span>, package <span class="op">=</span> <span class="st">"sigminer"</span><span class="op">)</span></span>
<span><span class="va">db1</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/readRDS.html">readRDS</a></span><span class="op">(</span><span class="va">db1</span><span class="op">)</span></span>
<span><span class="fu"><a href="https://rdrr.io/r/base/colnames.html">colnames</a></span><span class="op">(</span><span class="va">db1</span><span class="op">)</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span><span class="op">(</span><span class="st">"Cancer type"</span>, <span class="st">"Signature Index"</span><span class="op">)</span></span>
<span><span class="va">db2</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.file.html">system.file</a></span><span class="op">(</span><span class="st">"extdata"</span>, <span class="st">"signature_record_by_cancer.rds"</span>, package <span class="op">=</span> <span class="st">"sigminer"</span><span class="op">)</span></span>
<span><span class="va">db2</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/readRDS.html">readRDS</a></span><span class="op">(</span><span class="va">db2</span><span class="op">)</span></span>
<span><span class="fu"><a href="https://rdrr.io/r/base/colnames.html">colnames</a></span><span class="op">(</span><span class="va">db2</span><span class="op">)</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span><span class="op">(</span></span>
<span>  <span class="st">"Cancer type"</span>, <span class="st">"Cohort"</span>, <span class="st">"Sequencing strategy"</span>,</span>
<span>  <span class="st">"SBS signature index"</span>,</span>
<span>  <span class="st">"DBS signature index"</span>,</span>
<span>  <span class="st">"ID signature index"</span></span>
<span><span class="op">)</span></span></code></pre></div>
<div class="sourceCode" id="cb89"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu">DT</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/pkg/DT/man/datatable.html">datatable</a></span><span class="op">(</span><span class="va">db1</span>, caption <span class="op">=</span> <span class="st">"Data source: https://cancer.sanger.ac.uk/signatures_v2/matrix.png"</span><span class="op">)</span></span></code></pre></div>
<div id="htmlwidget-b714af026b82d92b1542" style="width:100%;height:auto;" class="datatables html-widget"></div>
<script type="application/json" data-for="htmlwidget-b714af026b82d92b1542">{"x":{"filter":"none","vertical":false,"caption":"<caption>Data source: https://cancer.sanger.ac.uk/signatures_v2/matrix.png<\/caption>","data":[["1","2","3","4","5","6","7","8","9","10","11","12","13","14","15","16","17","18","19","20","21","22","23","24","25","26","27","28","29","30","31","32","33","34","35","36","37","38","39","40"],["Adrenocortical carcinoma","Acute lymphoblastic leukemia","Acute myelogenous leukemia","Bladder","Breast","Cervix","Chondrosarcoma","B-cell chronic lymphocytic leukemia","Colorectum","Glioblastoma","Glioma Low grade","Head and neck","Kidney Chromophobe","Kidney Clear Cell","Kidney Papillary","Liver","Lung Adeno","Lung Small Cell","Lung Squamous","Lymphoma B-cell","Lymphoma Hodgkin","Medulloblastoma","Melanoma","Masopharyngeal Carcinoma","Masopharyngeal Carcinoma","Neuroblastoma","Oesophagus","Oral gingivo-buccal squamous","Osteosarcoma","Ovary","Pancreas","Paraganglioma","Pilocytic Astrocytoma","Prostate","Stomach","Thyroid","Urothelial Carcinoma","Uterine Carcinoma","Uterine Carcinosarcoma","Uveal Melanoma"],["1,2,4,5,6,13,18","1,2,5,13","1,5","1,2,5,10,13","1,2,3,5,6,8,10,13,17,18,20,26,30","1,2,5,6,10,13,26","1,5","1,2,5,9,13","1,5,6,10","1,5,11","1,5,6,14","1,2,4,5,7,13","1,5,6","1,5,6,27","1,2,5,13","1,4,5,6,12,16,17,22,23,24","1,2,4,5,6,13,17","1,4,5,15","1,2,4,5,13","1,2,5,9,13,17","1,5,25","1,5,8","1,5,7,11,17","1,2,5,13","1,2,5,6,13","1,5,18","1,2,4,5,6,13,17","1,2,5,7,13,29","1,2,5,6,13,30","1,3,5","1,2,3,5,6,13","1,5","1,5,19","1,5,6","1,2,5,13,15,17,18,20,21,26,28","1,2,5,13","1,2,5,13,22","1,2,5,6,10,13,14,26","1,2,5,6,10,13","1,5,6"]],"container":"<table class=\"display\">\n  <thead>\n    <tr>\n      <th> <\/th>\n      <th>Cancer type<\/th>\n      <th>Signature Index<\/th>\n    <\/tr>\n  <\/thead>\n<\/table>","options":{"columnDefs":[{"orderable":false,"targets":0}],"order":[],"autoWidth":false,"orderClasses":false}},"evals":[],"jsHooks":[]}</script><blockquote>
<p>Note, set <code>sig_db</code> to ‘legacy’ (the default) in <code><a href="https://rdrr.io/pkg/sigminer/man/sig_fit.html">sig_fit()</a></code> family functions.</p>
</blockquote>
<div class="sourceCode" id="cb90"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu">DT</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/pkg/DT/man/datatable.html">datatable</a></span><span class="op">(</span><span class="va">db2</span><span class="op">[</span>, <span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span><span class="op">(</span><span class="fl">1</span><span class="op">:</span><span class="fl">3</span>, <span class="fl">4</span><span class="op">)</span><span class="op">]</span>, caption <span class="op">=</span> <span class="st">"Data source: Alexandrov et al. https://www.nature.com/articles/s41586-020-1943-3"</span><span class="op">)</span></span></code></pre></div>
<div id="htmlwidget-2ea5ee496f245912dc4f" style="width:100%;height:auto;" class="datatables html-widget"></div>
<script type="application/json" data-for="htmlwidget-2ea5ee496f245912dc4f">{"x":{"filter":"none","vertical":false,"caption":"<caption>Data source: Alexandrov et al. https://www.nature.com/articles/s41586-020-1943-3<\/caption>","data":[["1","2","3","4","5","6","7","8","9","10","11","12","13","14","15","16","17","18","19","20","21","22","23","24","25","26","27","28","29","30","31","32","33","34","35","36","37","38","39","40","41","42","43","44","45","46","47","48","49","50","51","52","53","54","55","56","57","58","59","60","61","62","63","64","65","66","67","68","69","70","71","72","73","74","75","76","77","78","79","80","81","82","83","84","85","86","87","88","89","90","91","92","93","94","95","96","97","98","99","100","101","102","103","104","105","106","107","108","109","110","111","112","113","114","115","116","117","118","119","120","121","122","123","124","125","126","127","128","129","130","131","132","133","134","135","136","137","138","139","140","141","142","143","144","145","146","147","148","149","150","151","152","153","154","155","156"],["Biliary-AdenoCA","Bladder-TCC","Bone-Benign","Bone-Epith","Bone-Osteosarc","Breast-AdenoCA","Breast-DCIS","Breast-LobularCA","CNS-GBM","CNS-Medullo","CNS-Oligo","CNS-PiloAstro","Cervix-AdenoCA","Cervix-SCC","ColoRect-AdenoCA","Eso-AdenoCA","Head-SCC","Kidney-ChRCC","Kidney-RCC","Liver-HCC","Lung-AdenoCA","Lung-SCC","Lymph-BNHL","Lymph-CLL","Myeloid-AML","Myeloid-MDS","Myeloid-MPN","Ovary-AdenoCA","Panc-AdenoCA","Panc-Endocrine","Prost-AdenoCA","Skin-Melanoma","SoftTissue-Leiomyo","SoftTissue-Liposarc","Stomach-AdenoCA","Thy-AdenoCA","Uterus-AdenoCA","ALL","AML","Adrenal-neoplasm","Biliary-AdenoCa","Bladder-TCC","Blood-CMDI","Breast-Fibroadenoma","Breast-cancer","CNS-GBM","CNS-LGG","CNS-Medullo","CNS-glioma-NOS","ColoRect-AdenoCa","ColoRect-Adenoma","Eso-AdenoCa","Eso-SCC","Ewings","Eye-Melanoma","Eye-RB","Head-SCC","Kidney-ChRCC","Kidney-NOS","Kidney-Papillary","Kidney-RCC","Kidney-Wilms","Liver-Benign","Liver-HCC","Lung-AdenoCa","Lung-Carcinoid","Lung-NOS","Lung-SCC","Lung-Small","Lymph-BNHL","Lymph-CLL","Lymph-NOS","Lymph-TNHL","Lymph-cHL","Meninges-Meningioma","Mesothelium-Mesothelioma","Neuroblastoma","Oral-SCC","Ovary-AdenoCa","Panc-AdenoCa","Panc-Endocrine","Panc-Other","Para-AdenoCa","Para-Adenoma","Pit-All","Prost-AdenoCa","Prost-Adenoma","Sarcoma-bone","Sarcoma","Skin-BCC","Skin-Melanoma","Skin-SCC","Small-Intestine-carcinoid","Stomach-AdenoCa","Testis-Ca","Thy-AdenoCa","Uterus-AdenoCa","ALL","AML","Biliary-AdenoCa","Blood-CMDI","Bone-cancer","Breast-cancer","CNS-GBM","CNS-LGG","CNS-Medullo","CNS-glioma-NOS","ColoRect-AdenoCa","Eso-AdenoCa","Ewings","Eye-Melanoma","Kidney-RCC","Liver-HCC","Lung-AdenoCa","Lymph-BNHL","Lymph-CLL","Ovary-AdenoCa","Panc-AdenoCa","Panc-Endocrine","Prost-AdenoCa","Sarcoma-bone","Sarcoma","Skin-Melanoma","Stomach-AdenoCa","AML","Adrenal-neoplasm","Biliary-AdenoCa","Breast-cancer","CNS-GBM","Cervix-CA","ColoRect-AdenoCa","DLBC","Eso-AdenoCa","Eye-Melanoma","Head-SCC","Kidney-ChRCC","Kidney-Papillary","Kidney-RCC","Liver-HCC","Lung-AdenoCa","Lung-SCC","Lymph-BNHL","Mesothelium-Mesothelioma","Ovary-AdenoCa","Panc-AdenoCa","Pheochromocytoma","Prost-AdenoCa","Sarcoma","Skin-Melanoma","Stomach-AdenoCa","Testis-Ca","Thy-AdenoCa","Thymoma","Transitional-cell-carcinoma","UCS","Uterus-AdenoCa"],["PCAWG","PCAWG","PCAWG","PCAWG","PCAWG","PCAWG","PCAWG","PCAWG","PCAWG","PCAWG","PCAWG","PCAWG","PCAWG","PCAWG","PCAWG","PCAWG","PCAWG","PCAWG","PCAWG","PCAWG","PCAWG","PCAWG","PCAWG","PCAWG","PCAWG","PCAWG","PCAWG","PCAWG","PCAWG","PCAWG","PCAWG","PCAWG","PCAWG","PCAWG","PCAWG","PCAWG","PCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","TCGA","TCGA","TCGA","TCGA","TCGA","TCGA","TCGA","TCGA","TCGA","TCGA","TCGA","TCGA","TCGA","TCGA","TCGA","TCGA","TCGA","TCGA","TCGA","TCGA","TCGA","TCGA","TCGA","TCGA","TCGA","TCGA","TCGA","TCGA","TCGA","TCGA","TCGA","TCGA"],["WGS","WGS","WGS","WGS","WGS","WGS","WGS","WGS","WGS","WGS","WGS","WGS","WGS","WGS","WGS","WGS","WGS","WGS","WGS","WGS","WGS","WGS","WGS","WGS","WGS","WGS","WGS","WGS","WGS","WGS","WGS","WGS","WGS","WGS","WGS","WGS","WGS","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WGS","WGS","WGS","WGS","WGS","WGS","WGS","WGS","WGS","WGS","WGS","WGS","WGS","WGS","WGS","WGS","WGS","WGS","WGS","WGS","WGS","WGS","WGS","WGS","WGS","WGS","WGS","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES"],["1,2,3,5,9,12,13,15,17a,17b,18,21,22,24,32,40,44","1,2,5,8,13,29,40","1,2,5,8,13,40,51,60","1,2,5,13,17a,17b,40","1,2,3,5,8,13,17a,17b,30,40","1,2,3,5,8,9,13,17a,17b,18,37,40,41","1,5,40","1,2,3,5,13,18","1,5,11,30,37,40","1,5,8,18,39,40,60","1,5,8,40","1,5,19,23,40","1,2,5,13","1,2,5,13,18,40","1,5,10a,10b,15,17a,17b,18,28,37,40,44,45","1,2,3,5,13,17a,17b,18,28,40","1,2,3,4,5,7a,7b,7d,13,16,17a,17b,18,33,40","1,2,5,13,17a,17b,29,40","1,2,5,13,22,29,40,41","1,4,5,6,9,12,14,16,17a,17b,18,19,22,24,26,28,29,30,31,35,40,53,54,56","1,2,3,4,5,9,13,17a,17b,18,28,40","1,2,4,5,8,13","1,2,3,5,6,9,13,17a,17b,34,36,37,40,56","1,5,9,40","1,5,18,31,60","1,5,23","1,2,5,19,23,32,51,58,60","1,2,3,5,8,13,18,26,35,39,40,41","1,2,3,5,6,8,13,17a,17b,18,20,26,28,30,40,51","1,2,3,5,6,8,9,11,13,26,30,36,39","1,2,3,5,8,13,18,33,37,40,41,45,52,58","1,2,5,7a,7b,7c,7d,13,17a,17b,38,40,58","1,2,5,13,17a,17b,30,40","1,2,3,5,13,37,40","1,2,3,5,9,13,15,17a,17b,18,20,21,26,28,40,41,43,44,51,58","1,2,5,13,40,58","1,2,3,5,6,10a,10b,13,14,15,26,28,40,44","1,2,4,5,6,7a,7b,7c,7d,8,9,10a,10b,11,12,13,14,15,16,17a,17b,18,19,20,21,22,24,26,27,28,29,30,31,32,33,34,36,37,38,40,42,43,44,46,48,49,50,51,52,54,56,57,58,59,60","1,2,3,4,5,6,7a,7b,7c,7d,8,9,10a,10b,11,13,15,16,17b,18,19,20,21,22,23,24,27,28,30,31,32,33,34,36,38,39,40,41,42,43,44,46,47,48,49,50,51,52,53,54,57,58,59","1,2,3,4,5,6,7a,7b,7c,7d,8,9,10a,10b,12,13,15,16,17a,17b,18,19,20,21,22,23,24,27,28,29,30,31,32,33,34,35,36,37,38,39,42,43,44,46,48,49,50,51,52,53,54,55,57,58,59,60","1,2,3,4,5,7a,7b,7c,7d,9,10a,10b,12,13,15,16,17a,17b,18,19,20,21,22,23,25,28,29,31,33,34,35,38,40,42,43,46,47,49,50,51,52,53,54,56,57,58,60","1,2,5,6,7d,10a,10b,11,13,15,16,18,21,22,23,29,31,39,40,42,43,44,45,49,50,52,54,55,59,60","1,2,3,4,5,6,7a,7b,7c,7d,8,9,10a,10b,11,13,14,15,16,17a,17b,19,20,21,22,23,24,26,27,29,30,31,32,33,34,36,37,38,39,42,43,44,46,48,49,50,51,52,53,54,56,57,58,59,60","1,2,8,18,31,32,42,50","1,2,3,5,6,7a,7b,7c,7d,8,10a,10b,13,14,15,16,17a,17b,18,19,20,21,22,26,30,31,32,33,34,35,36,37,38,39,40,41,42,44,46,48,49,50,52,54,56,57,58,59","1,2,3,5,6,7a,7b,7c,7d,8,10a,10b,11,13,15,16,17a,17b,18,19,20,21,22,24,25,29,30,31,32,34,35,36,38,39,40,41,42,43,45,46,48,49,51,54,57,58,59","1,2,3,4,5,6,7a,7b,7c,7d,10a,10b,11,13,14,15,16,17a,17b,18,19,20,22,24,25,28,30,31,32,33,34,36,37,38,39,41,42,43,44,45,46,47,48,49,50,51,52,54,56,57,58,59,60","1,2,3,5,6,7a,7b,7c,7d,8,10a,10b,13,14,15,16,17a,17b,18,19,20,21,22,23,24,26,28,30,31,32,33,34,36,37,38,39,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60","1,2,4,5,7a,7b,7c,7d,8,10a,10b,11,13,15,16,17a,19,21,22,24,25,28,30,31,32,35,39,40,42,43,46,50,52,57,58,59,60","1,2,4,5,6,7a,7b,7c,8,9,10a,10b,11,12,13,14,15,16,17a,17b,18,19,20,21,22,24,26,28,29,30,31,32,34,36,38,39,40,42,43,44,45,46,48,49,50,52,53,54,55,56,58,59","1,2,5,10a,10b,14,15,18,22,25,29,48","1,2,4,5,6,7a,7b,7c,7d,10a,10b,13,14,15,16,17a,17b,18,19,24,30,31,38,39,41,44,45,50,58","1,2,3,4,5,6,7a,7c,7d,9,10a,10b,11,12,13,14,15,16,17a,17b,18,19,22,23,24,25,29,30,31,33,34,35,36,39,40,42,43,44,46,48,50,51,52,54,57,58,59,60","1,2,3,5,6,7a,7b,7c,7d,8,10a,10b,11,13,15,16,17a,17b,18,19,20,22,23,24,25,27,28,30,31,32,33,34,35,39,41,42,44,46,48,49,50,51,52,53,56,57,58,59","1,2,3,5,6,7a,7b,7d,9,10a,10b,13,15,16,17a,17b,19,21,22,23,28,29,31,32,38,39,40,42,44,48,49,50,51,52,54,58,59","1,2,5,15,39,50,59","1,2,3,4,5,6,7a,7b,7c,7d,8,10a,10b,13,14,15,16,17a,17b,18,19,20,21,22,23,24,26,27,28,29,30,31,32,33,34,36,38,42,43,44,46,48,49,50,51,52,53,54,57,58,59","1,2,3,4,5,6,7a,7b,7c,7d,8,9,10a,10b,13,14,15,16,17a,22,23,28,38,40,42,45,46,48,51,52,53,54,55,57,58,59,60","1,2,3,5,7a,7b,7c,7d,10a,13,14,15,16,17a,17b,22,28,29,31,32,33,38,40,42,49,50,51,52,54,56,58,59","1,5,9,10a,10b,12,13,15,16,17a,17b,18,19,20,21,22,25,26,27,28,31,37,38,40,56","1,2,3,4,5,7a,7b,7c,7d,8,10a,10b,13,14,15,16,17a,17b,18,19,20,21,22,24,25,26,27,28,29,31,32,33,35,36,37,38,39,40,42,43,44,46,47,48,50,51,52,53,54,56,57,58,59","1,5,6,7a,10b,13,14,15,21,23,24,29,31,39,49,50,52,54,57,58,60","1,2,3,5,7b,7c,7d,10b,13,15,17a,17b,19,24,25,26,29,30,31,33,35,36,37,38,42,44,49,50,51,53,54,57,58,59","1,2,3,4,5,7a,7b,7c,7d,8,10a,10b,11,12,13,14,15,16,17a,17b,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,42,45,47,48,49,50,51,52,53,54,55,56,57,58,59","1,2,3,4,5,6,7a,7b,7c,7d,9,10a,10b,12,13,14,15,16,17a,17b,18,19,20,21,22,23,24,26,27,28,29,30,31,32,33,35,36,37,38,42,43,44,45,46,48,49,50,51,52,53,54,56,57,58,59,60","1,2,3,4,5,7d,10a,10b,12,13,15,16,17b,18,19,20,21,25,27,28,31,32,39,42,48,50,52,53,54,56,57,58,59","1,2,3,4,5,7a,7c,7d,10a,10b,11,13,14,18,29,31,35,36,38,39,40,50,59","1,2,3,4,5,7a,7d,8,10a,10b,12,13,15,16,17b,21,22,24,25,26,27,28,30,31,33,34,37,38,40,43,45,49,50,51,53,54,55,58,60","1,2,4,5,13,15,16,18,29,35,36,40,44,45,49","1,2,3,4,5,6,7a,7b,7c,7d,8,9,10a,10b,11,12,13,14,15,16,17a,17b,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,42,43,44,45,46,47,48,49,50,51,52,53,54,55,57,58,59,60","1,2,3,5,7a,7b,7c,7d,8,10a,10b,13,15,16,17a,17b,19,20,21,22,24,25,26,27,28,31,32,33,34,39,40,42,43,44,48,49,50,51,52,54,55,57,58,59,60","1,5,6,7a,7c,10a,10b,11,13,15,17b,19,24,25,31,32,38,39,40,42,44,50,55,57,59","1,5,7a,10a,10b,13,16,17a,17b,21,30,31,42,50,58","1,2,5,13","1,2,5,6,7a,7b,7c,7d,9,10a,10b,13,14,15,16,19,20,21,22,23,27,28,30,31,32,33,34,38,39,40,42,44,45,46,48,49,52,53,57,58,59","1,2,4,5,10a,10b,13,15,16,17a,17b,22,31,40,42,58","1,2,3,4,5,6,7a,7c,7d,8,10a,10b,11,13,14,15,16,17a,17b,18,19,20,22,23,24,25,27,28,29,30,31,32,33,34,35,36,37,38,39,42,43,44,45,48,49,50,51,52,53,54,56,57,58,59,60","1,2,5,7a,7b,7c,7d,10b,13,14,18,20,29,48,49,59","1,2,4,5,6,7a,7b,10a,10b,13,15,17a,18,20,32,40,42,51,59","1,2,4,5,6,7a,7b,7c,7d,8,9,10a,10b,11,13,14,15,16,17a,17b,18,19,20,21,22,24,26,28,29,30,31,32,33,35,38,39,40,42,43,44,46,47,48,49,50,51,52,53,54,56,57,58,59","1,5,7a,7b,7c,10b,13,17a,17b,24,31,39,40,52,53,58","1,2,5,7a,7b,7c,7d,8,10a,10b,13,15,16,27,31,32,34,39,40,42,44,50,51,54,57,59,60","1,2,3,5,7a,7b,7c,7d,13,19,42,46","1,2,5,6,7a,7b,7d,10b,15,17a,17b,19,21,28,32,37,38,42,59","1,5,6,10b,13,15,42","1,2,3,5,6,7a,7b,7c,7d,8,10a,10b,12,13,15,17a,17b,18,19,21,24,29,31,36,37,38,40,41,42,44,48,50,51,52,53,56,57","1,2,4,5,7a,7c,7d,10a,10b,13,15,16,17a,18,19,20,28,29,31,39,42,48,49,52,58,59","1,2,4,5,7a,7b,7c,7d,10a,10b,13,14,15,18,19,20,21,22,25,27,28,31,32,39,40,42,48,50,51,53,55,57,58,59","1,2,3,4,5,7a,7b,7c,7d,8,9,10a,10b,13,14,15,16,17a,17b,18,19,21,22,23,24,25,27,28,29,30,31,32,34,35,36,37,39,42,43,44,48,50,53,54,55,56,57,58,59","1,2,5,7a,7b,7c,7d,11,12,16,19,42,58","1,2,3,5,7a,7b,7c,7d,10a,10b,11,13,15,16,17a,17b,19,20,21,22,23,24,25,30,31,32,33,34,37,38,39,40,42,43,48,49,50,52,53,54,58,59,60","1,2,4,5,6,7a,7b,7c,7d,13,38,40","1,5,7a,10a,10b,12,13,15,16,17b,21,22,24,25,31,32,33,35,37,39,42,50,51,52,54,57,58,59,60","1,2,3,5,7a,7b,7c,7d,10a,10b,13,14,15,17a,17b,18,19,20,28,29,36,39,40,42,43,44,45,47,54,58,59,60","1,2,4,5,7a,7b,7c,7d,10a,10b,13,16,17a,17b,19,24,29,30,31,32,34,37,38,39,40,42,44,46,47,49,50,53,54,56,57,59","1,2,5,6,8,13,14,15,16,19,29,30,40,42,43,48,51,54,57,59","1,2,5,10a,10b,13,15,17a,17b,30,32,57","1,2,5,7a,7b,7c,7d,13,18,40","1,5,19,40","1,2,5,13,17a,17b,18,20,22,40,44","1,5,39","1,5,8","1,2,3,5,8,13,17a,17b,18,21,26,30,34,39,41,44,60","1,5,15,37,40","1,5,10a,10b,19,34,51,52","1,3,5,8,40,60","1,5,10b,40","1,5,18,40,41","1,2,5,6,13,17a,17b,18,20,26,34,40","1,2,5,7a,7b,7c,7d,8,13,14,17b,18,20,35,39,40,57","1,5,7b,7c,7d,23,35,40,51,52,57","1,4,5,12,22,40,57","1,3,5,12,16,18,22,24,29,35,46,58","1,2,3,4,5,13,40,46,58","1,5,9,40","1,5,8,9,18,40,43,47,51","1,2,3,5,8,13,39,40","1,2,3,5,13,16,17a,17b,18,31,34,37,40,44,56,58,60","1,5,17a,17b,40,58","1,5,8,18,39,40,43,58","1,2,5,7a,7b,7c,7d,13,14,18,35,40","1,5,18,40","1,2,5,7a,7b,7c,7d,9,13,38,40,43,55,58","1,2,3,5,8,13,15,17a,17b,18,26,28,34,44,57","1,2,4,5,6,7a,7c,10a,10b,11,15,17a,17b,18,19,20,24,27,29,30,31,32,33,34,38,40,42,43,45,47,49,50,51,52,53,54,56,57,58,59,60","1,2,3,4,5,6,7a,7d,10b,13,15,16,17a,20,21,22,23,24,32,35,36,38,42,43,44,46,49,50,57,58,59","1,2,5,7b,10b,13,16,17a,17b,18,20,28,29,32,36,40,42,44,58","1,2,3,5,6,7a,7b,7c,7d,10a,10b,11,13,14,15,16,17a,18,19,20,21,22,23,25,26,28,29,30,31,32,33,34,36,38,42,44,45,47,48,49,50,51,52,54,56,57,58,59,60","1,2,5,7a,7b,10a,10b,13,15,16,21,27,29,30,31,40,42,45,54,59","1,2,3,5,6,10a,10b,13,15,17a,17b,26,28,33,40,44,45,50,59","1,2,3,5,9,10a,10b,13,15,17a,17b,20,26,30,40,44,49","1,2,5,6,7a,7b,7c,7d,10a,10b,11,13,14,15,16,19,20,21,23,26,30,31,33,35,36,37,39,42,45,46,48,49,50,52,53,54,57,58,59,60","1,2,3,4,5,6,8,10a,10b,13,15,16,17a,17b,18,42,44,45","1,2,3,5,7a,7b,7c,7d,10a,10b,11,13,14,15,16,17a,19,20,21,22,23,24,25,28,31,32,33,37,38,39,42,44,48,49,52,53,54,57,58,59,60","1,2,4,5,7a,7b,7c,7d,10a,10b,13,15,16,19,21,24,29,31,33,35,36,38,39,40,44,45,49,50","1,2,3,5,7a,7b,7d,8,10b,12,13,15,17a,18,22,24,32,33,34,40,46,50,51","1,2,3,5,7a,7b,7c,7d,8,9,10a,10b,12,13,14,15,16,17a,17b,18,19,20,22,25,26,27,29,30,31,32,33,35,36,37,40,42,43,45,46,48,49,50,52,59","1,2,5,7a,7b,7c,7d,10a,10b,12,14,15,17a,17b,19,20,21,22,23,25,26,29,30,31,32,39,40,42,44,45,46,48,49,51,52,54,56,58,59","1,2,4,5,6,8,9,10a,10b,14,15,16,17a,19,20,22,24,25,29,30,31,32,40,42,45,46,48,49,53,54,59","1,2,3,4,5,6,7a,7b,7c,7d,8,10a,10b,11,13,15,17a,17b,18,19,20,21,22,23,24,25,26,29,30,32,35,36,40,42,45,48,49,52,53,54,58,59","1,2,3,4,5,7a,7b,7c,7d,8,10a,10b,13,15,17a,18,19,24,29,30,35,36,38,40,45,49,50,52,54","1,2,5,6,7a,7c,13,17a,17b,40,42","1,2,5,6,7a,10a,10b,15,19,30,31,33,35,38,40,48,49,52,54,58,59","1,2,3,4,5,6,7a,7b,7c,7d,8,10a,10b,13,14,15,16,18,22,23,27,28,29,30,31,32,35,36,38,39,40,42,43,45,49,50,51,52,53,56,57,58,59","1,2,3,5,6,7a,7b,7d,10a,10b,13,14,15,17a,17b,24,31,32,34,40,44,46,48,50,52,54,58,60","1,2,3,5,6,7a,7b,7c,7d,10a,10b,11,12,13,15,16,17a,17b,18,19,21,23,24,26,27,28,29,30,31,32,33,35,36,38,39,40,42,44,45,46,48,49,50,52,53,54,56,57,58,59,60","1,2,5,6,7a,7b,7c,7d,10a,10b,11,13,15,16,17a,17b,19,21,22,25,28,30,31,32,34,40,41,42,45,46,48,49,50,52,54,56,58,59","1,2,3,4,5,7a,7b,7c,7d,8,10a,10b,11,13,14,15,16,17a,18,19,20,22,24,25,28,29,30,31,32,35,36,38,39,40,42,45,48,49,50,51,52,56,58,59","1,2,5,7a,7b,7c,7d,10a,10b,13,14,15,17a,17b,28,32,36,38,39,42,45,49,52,54,55,60","1,2,5,6,10a,10b,13,14,15,17a,17b,20,21,22,28,30,40,42,45,48,50,54,56,58","1,2,3,4,5,6,7a,7b,7c,7d,10a,10b,12,13,15,16,17a,17b,18,19,20,23,24,26,28,29,30,31,32,34,35,38,39,40,42,43,44,45,49,50,52,53,54,56,57,58,59,60","1,2,3,5,6,7a,7b,7c,7d,10a,10b,11,12,13,14,15,16,17a,17b,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,38,39,40,42,43,44,45,46,48,49,50,51,52,53,54,55,56,57,58,59,60","1,2,3,4,5,6,7a,7b,7c,7d,8,10a,10b,11,13,14,15,16,17a,18,19,20,21,23,24,27,28,29,30,36,37,38,40,42,44,45,46,47,48,49,50,52,53,54,56,58,59","1,2,3,5,7b,7d,10a,10b,13,15,18,19,22,23,29,37,45,46,52","1,2,5,7c,7d,10a,10b,13,14,18,40,44","1,2,5,7a,7b,7d,10a,10b,13,14,15,17a,20,21,26,28,30,39,40,44,54"]],"container":"<table class=\"display\">\n  <thead>\n    <tr>\n      <th> <\/th>\n      <th>Cancer type<\/th>\n      <th>Cohort<\/th>\n      <th>Sequencing strategy<\/th>\n      <th>SBS signature index<\/th>\n    <\/tr>\n  <\/thead>\n<\/table>","options":{"columnDefs":[{"orderable":false,"targets":0}],"order":[],"autoWidth":false,"orderClasses":false}},"evals":[],"jsHooks":[]}</script><div class="sourceCode" id="cb91"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu">DT</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/pkg/DT/man/datatable.html">datatable</a></span><span class="op">(</span><span class="va">db2</span><span class="op">[</span>, <span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span><span class="op">(</span><span class="fl">1</span><span class="op">:</span><span class="fl">3</span>, <span class="fl">5</span><span class="op">)</span><span class="op">]</span>, caption <span class="op">=</span> <span class="st">"Data source: Alexandrov et al. https://www.nature.com/articles/s41586-020-1943-3"</span><span class="op">)</span></span></code></pre></div>
<div id="htmlwidget-196cd27525533b48d303" style="width:100%;height:auto;" class="datatables html-widget"></div>
<script type="application/json" data-for="htmlwidget-196cd27525533b48d303">{"x":{"filter":"none","vertical":false,"caption":"<caption>Data source: Alexandrov et al. https://www.nature.com/articles/s41586-020-1943-3<\/caption>","data":[["1","2","3","4","5","6","7","8","9","10","11","12","13","14","15","16","17","18","19","20","21","22","23","24","25","26","27","28","29","30","31","32","33","34","35","36","37","38","39","40","41","42","43","44","45","46","47","48","49","50","51","52","53","54","55","56","57","58","59","60","61","62","63","64","65","66","67","68","69","70","71","72","73","74","75","76","77","78","79","80","81","82","83","84","85","86","87","88","89","90","91","92","93","94","95","96","97","98","99","100","101","102","103","104","105","106","107","108","109","110","111","112","113","114","115","116","117","118","119","120","121","122","123","124","125","126","127","128","129","130","131","132","133","134","135","136","137","138","139","140","141","142","143","144","145","146","147","148","149","150","151","152","153","154","155","156"],["Biliary-AdenoCA","Bladder-TCC","Bone-Benign","Bone-Epith","Bone-Osteosarc","Breast-AdenoCA","Breast-DCIS","Breast-LobularCA","CNS-GBM","CNS-Medullo","CNS-Oligo","CNS-PiloAstro","Cervix-AdenoCA","Cervix-SCC","ColoRect-AdenoCA","Eso-AdenoCA","Head-SCC","Kidney-ChRCC","Kidney-RCC","Liver-HCC","Lung-AdenoCA","Lung-SCC","Lymph-BNHL","Lymph-CLL","Myeloid-AML","Myeloid-MDS","Myeloid-MPN","Ovary-AdenoCA","Panc-AdenoCA","Panc-Endocrine","Prost-AdenoCA","Skin-Melanoma","SoftTissue-Leiomyo","SoftTissue-Liposarc","Stomach-AdenoCA","Thy-AdenoCA","Uterus-AdenoCA","ALL","AML","Adrenal-neoplasm","Biliary-AdenoCa","Bladder-TCC","Blood-CMDI","Breast-Fibroadenoma","Breast-cancer","CNS-GBM","CNS-LGG","CNS-Medullo","CNS-glioma-NOS","ColoRect-AdenoCa","ColoRect-Adenoma","Eso-AdenoCa","Eso-SCC","Ewings","Eye-Melanoma","Eye-RB","Head-SCC","Kidney-ChRCC","Kidney-NOS","Kidney-Papillary","Kidney-RCC","Kidney-Wilms","Liver-Benign","Liver-HCC","Lung-AdenoCa","Lung-Carcinoid","Lung-NOS","Lung-SCC","Lung-Small","Lymph-BNHL","Lymph-CLL","Lymph-NOS","Lymph-TNHL","Lymph-cHL","Meninges-Meningioma","Mesothelium-Mesothelioma","Neuroblastoma","Oral-SCC","Ovary-AdenoCa","Panc-AdenoCa","Panc-Endocrine","Panc-Other","Para-AdenoCa","Para-Adenoma","Pit-All","Prost-AdenoCa","Prost-Adenoma","Sarcoma-bone","Sarcoma","Skin-BCC","Skin-Melanoma","Skin-SCC","Small-Intestine-carcinoid","Stomach-AdenoCa","Testis-Ca","Thy-AdenoCa","Uterus-AdenoCa","ALL","AML","Biliary-AdenoCa","Blood-CMDI","Bone-cancer","Breast-cancer","CNS-GBM","CNS-LGG","CNS-Medullo","CNS-glioma-NOS","ColoRect-AdenoCa","Eso-AdenoCa","Ewings","Eye-Melanoma","Kidney-RCC","Liver-HCC","Lung-AdenoCa","Lymph-BNHL","Lymph-CLL","Ovary-AdenoCa","Panc-AdenoCa","Panc-Endocrine","Prost-AdenoCa","Sarcoma-bone","Sarcoma","Skin-Melanoma","Stomach-AdenoCa","AML","Adrenal-neoplasm","Biliary-AdenoCa","Breast-cancer","CNS-GBM","Cervix-CA","ColoRect-AdenoCa","DLBC","Eso-AdenoCa","Eye-Melanoma","Head-SCC","Kidney-ChRCC","Kidney-Papillary","Kidney-RCC","Liver-HCC","Lung-AdenoCa","Lung-SCC","Lymph-BNHL","Mesothelium-Mesothelioma","Ovary-AdenoCa","Panc-AdenoCa","Pheochromocytoma","Prost-AdenoCa","Sarcoma","Skin-Melanoma","Stomach-AdenoCa","Testis-Ca","Thy-AdenoCa","Thymoma","Transitional-cell-carcinoma","UCS","Uterus-AdenoCa"],["PCAWG","PCAWG","PCAWG","PCAWG","PCAWG","PCAWG","PCAWG","PCAWG","PCAWG","PCAWG","PCAWG","PCAWG","PCAWG","PCAWG","PCAWG","PCAWG","PCAWG","PCAWG","PCAWG","PCAWG","PCAWG","PCAWG","PCAWG","PCAWG","PCAWG","PCAWG","PCAWG","PCAWG","PCAWG","PCAWG","PCAWG","PCAWG","PCAWG","PCAWG","PCAWG","PCAWG","PCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","TCGA","TCGA","TCGA","TCGA","TCGA","TCGA","TCGA","TCGA","TCGA","TCGA","TCGA","TCGA","TCGA","TCGA","TCGA","TCGA","TCGA","TCGA","TCGA","TCGA","TCGA","TCGA","TCGA","TCGA","TCGA","TCGA","TCGA","TCGA","TCGA","TCGA","TCGA","TCGA"],["WGS","WGS","WGS","WGS","WGS","WGS","WGS","WGS","WGS","WGS","WGS","WGS","WGS","WGS","WGS","WGS","WGS","WGS","WGS","WGS","WGS","WGS","WGS","WGS","WGS","WGS","WGS","WGS","WGS","WGS","WGS","WGS","WGS","WGS","WGS","WGS","WGS","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WGS","WGS","WGS","WGS","WGS","WGS","WGS","WGS","WGS","WGS","WGS","WGS","WGS","WGS","WGS","WGS","WGS","WGS","WGS","WGS","WGS","WGS","WGS","WGS","WGS","WGS","WGS","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES"],["2,4,5,6,7,8,9,11","2,4,5,6,9,11","1,2,5,6,7,8,9,11","2,4,7,9,11","1,2,4,5,6,7,9,11","1,2,3,4,5,6,7,8,9,10,11","2,4,6","1,2,4,5,6,8,9,11","2,3,4,5,6,7,9,10,11","1,2,3,4,5,6,7,8,9,10,11","2,3,4,5,6,7,9,11","1,2,3,4,5,6,7,8,9,11","4,7,11","2,4,6,7,9,11","2,3,4,5,6,7,8,9,10,11","2,3,4,5,6,7,8,9,11","1,2,3,4,5,6,9,11","1,2,3,4,5,6,7,8,9,10,11","2,4,5,6,7,9,11","2,3,4,5,6,7,9,11","2,4,5,6,7,8,11","2,4,11","2,3,4,5,6,7,8,9,10,11","2,3,4,5,6,7,8,9,11","1,3,4,5,6,7,9","1,3","1,2,3,4,5,6,7,9,11","2,3,4,5,6,7,9,11","1,2,3,4,5,6,7,9,11","2,3,4,5,6,7,8,9,11","1,2,3,4,5,6,7,8,9,10,11","1,2,4,6,7,9,11","1,2,4,6,9,11","1,2,4,6,11","1,2,3,4,5,6,7,9,10,11","1,2,4,5,6,7,8,9,11","2,3,4,5,6,7,9,10,11",null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null]],"container":"<table class=\"display\">\n  <thead>\n    <tr>\n      <th> <\/th>\n      <th>Cancer type<\/th>\n      <th>Cohort<\/th>\n      <th>Sequencing strategy<\/th>\n      <th>DBS signature index<\/th>\n    <\/tr>\n  <\/thead>\n<\/table>","options":{"columnDefs":[{"orderable":false,"targets":0}],"order":[],"autoWidth":false,"orderClasses":false}},"evals":[],"jsHooks":[]}</script><div class="sourceCode" id="cb92"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu">DT</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/pkg/DT/man/datatable.html">datatable</a></span><span class="op">(</span><span class="va">db2</span><span class="op">[</span>, <span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span><span class="op">(</span><span class="fl">1</span><span class="op">:</span><span class="fl">3</span>, <span class="fl">6</span><span class="op">)</span><span class="op">]</span>, caption <span class="op">=</span> <span class="st">"Data source: Alexandrov et al. https://www.nature.com/articles/s41586-020-1943-3"</span><span class="op">)</span></span></code></pre></div>
<div id="htmlwidget-6cc68f31a4e6a40148cd" style="width:100%;height:auto;" class="datatables html-widget"></div>
<script type="application/json" data-for="htmlwidget-6cc68f31a4e6a40148cd">{"x":{"filter":"none","vertical":false,"caption":"<caption>Data source: Alexandrov et al. https://www.nature.com/articles/s41586-020-1943-3<\/caption>","data":[["1","2","3","4","5","6","7","8","9","10","11","12","13","14","15","16","17","18","19","20","21","22","23","24","25","26","27","28","29","30","31","32","33","34","35","36","37","38","39","40","41","42","43","44","45","46","47","48","49","50","51","52","53","54","55","56","57","58","59","60","61","62","63","64","65","66","67","68","69","70","71","72","73","74","75","76","77","78","79","80","81","82","83","84","85","86","87","88","89","90","91","92","93","94","95","96","97","98","99","100","101","102","103","104","105","106","107","108","109","110","111","112","113","114","115","116","117","118","119","120","121","122","123","124","125","126","127","128","129","130","131","132","133","134","135","136","137","138","139","140","141","142","143","144","145","146","147","148","149","150","151","152","153","154","155","156"],["Biliary-AdenoCA","Bladder-TCC","Bone-Benign","Bone-Epith","Bone-Osteosarc","Breast-AdenoCA","Breast-DCIS","Breast-LobularCA","CNS-GBM","CNS-Medullo","CNS-Oligo","CNS-PiloAstro","Cervix-AdenoCA","Cervix-SCC","ColoRect-AdenoCA","Eso-AdenoCA","Head-SCC","Kidney-ChRCC","Kidney-RCC","Liver-HCC","Lung-AdenoCA","Lung-SCC","Lymph-BNHL","Lymph-CLL","Myeloid-AML","Myeloid-MDS","Myeloid-MPN","Ovary-AdenoCA","Panc-AdenoCA","Panc-Endocrine","Prost-AdenoCA","Skin-Melanoma","SoftTissue-Leiomyo","SoftTissue-Liposarc","Stomach-AdenoCA","Thy-AdenoCA","Uterus-AdenoCA","ALL","AML","Adrenal-neoplasm","Biliary-AdenoCa","Bladder-TCC","Blood-CMDI","Breast-Fibroadenoma","Breast-cancer","CNS-GBM","CNS-LGG","CNS-Medullo","CNS-glioma-NOS","ColoRect-AdenoCa","ColoRect-Adenoma","Eso-AdenoCa","Eso-SCC","Ewings","Eye-Melanoma","Eye-RB","Head-SCC","Kidney-ChRCC","Kidney-NOS","Kidney-Papillary","Kidney-RCC","Kidney-Wilms","Liver-Benign","Liver-HCC","Lung-AdenoCa","Lung-Carcinoid","Lung-NOS","Lung-SCC","Lung-Small","Lymph-BNHL","Lymph-CLL","Lymph-NOS","Lymph-TNHL","Lymph-cHL","Meninges-Meningioma","Mesothelium-Mesothelioma","Neuroblastoma","Oral-SCC","Ovary-AdenoCa","Panc-AdenoCa","Panc-Endocrine","Panc-Other","Para-AdenoCa","Para-Adenoma","Pit-All","Prost-AdenoCa","Prost-Adenoma","Sarcoma-bone","Sarcoma","Skin-BCC","Skin-Melanoma","Skin-SCC","Small-Intestine-carcinoid","Stomach-AdenoCa","Testis-Ca","Thy-AdenoCa","Uterus-AdenoCa","ALL","AML","Biliary-AdenoCa","Blood-CMDI","Bone-cancer","Breast-cancer","CNS-GBM","CNS-LGG","CNS-Medullo","CNS-glioma-NOS","ColoRect-AdenoCa","Eso-AdenoCa","Ewings","Eye-Melanoma","Kidney-RCC","Liver-HCC","Lung-AdenoCa","Lymph-BNHL","Lymph-CLL","Ovary-AdenoCa","Panc-AdenoCa","Panc-Endocrine","Prost-AdenoCa","Sarcoma-bone","Sarcoma","Skin-Melanoma","Stomach-AdenoCa","AML","Adrenal-neoplasm","Biliary-AdenoCa","Breast-cancer","CNS-GBM","Cervix-CA","ColoRect-AdenoCa","DLBC","Eso-AdenoCa","Eye-Melanoma","Head-SCC","Kidney-ChRCC","Kidney-Papillary","Kidney-RCC","Liver-HCC","Lung-AdenoCa","Lung-SCC","Lymph-BNHL","Mesothelium-Mesothelioma","Ovary-AdenoCa","Panc-AdenoCa","Pheochromocytoma","Prost-AdenoCa","Sarcoma","Skin-Melanoma","Stomach-AdenoCa","Testis-Ca","Thy-AdenoCa","Thymoma","Transitional-cell-carcinoma","UCS","Uterus-AdenoCa"],["PCAWG","PCAWG","PCAWG","PCAWG","PCAWG","PCAWG","PCAWG","PCAWG","PCAWG","PCAWG","PCAWG","PCAWG","PCAWG","PCAWG","PCAWG","PCAWG","PCAWG","PCAWG","PCAWG","PCAWG","PCAWG","PCAWG","PCAWG","PCAWG","PCAWG","PCAWG","PCAWG","PCAWG","PCAWG","PCAWG","PCAWG","PCAWG","PCAWG","PCAWG","PCAWG","PCAWG","PCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","nonPCAWG","TCGA","TCGA","TCGA","TCGA","TCGA","TCGA","TCGA","TCGA","TCGA","TCGA","TCGA","TCGA","TCGA","TCGA","TCGA","TCGA","TCGA","TCGA","TCGA","TCGA","TCGA","TCGA","TCGA","TCGA","TCGA","TCGA","TCGA","TCGA","TCGA","TCGA","TCGA","TCGA"],["WGS","WGS","WGS","WGS","WGS","WGS","WGS","WGS","WGS","WGS","WGS","WGS","WGS","WGS","WGS","WGS","WGS","WGS","WGS","WGS","WGS","WGS","WGS","WGS","WGS","WGS","WGS","WGS","WGS","WGS","WGS","WGS","WGS","WGS","WGS","WGS","WGS","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WGS","WGS","WGS","WGS","WGS","WGS","WGS","WGS","WGS","WGS","WGS","WGS","WGS","WGS","WGS","WGS","WGS","WGS","WGS","WGS","WGS","WGS","WGS","WGS","WGS","WGS","WGS","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES","WES"],["1,2,3,5,6,8,11","1,2,3,4,5,8,9,10","1,2,5,6,9,10,12","1,2,5,8,9","1,2,3,4,5,8,9,14","1,2,4,5,6,8,9,11","1,5,8","1,2,5,6,8,9","1,2,4,5,8,9","1,2,5,8,9,10,12,14,16","1,2,4,5,8,9","1,2,3,4,5,6,8,9,10,11,12,14,17","1","1,2,6,9,10","1,2,5,14","1,2,4,5,6,8,9,10,14","1,2,3,5,6,8,9,10,11,12","1,2,3,4,5,6,8,9,11","1,2,3,4,5,6,8,9,11","1,2,3,5,6,8,9,11,13","1,2,3,5,6,8,9,12","1,2,3,6,8,9","1,2,4,5,6,8,9","1,2,4,5,8,9","1,2,3,5,9,10,11","1,3,5","1,2,3,4,5,6,7,8,9,10,11,16","1,2,4,5,6,8,9","1,2,5,6,8,9,10,11,12","1,2,3,4,5,6,8,9,10,11","1,2,3,4,5,6,7,8,9,10,11,12,13,17","1,2,4,5,8,9,13","1,2,5,8,9","1,2,3,5,8,9,12,14","1,2,3,4,5,6,7,8,9,12,13,14,17","1,2,3,4,5,8,9,10,12,13","1,2,4,6,8,9",null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,"1,2,3,15,16","1,2,3,4,7","8","1,2,6,7,15","1,2,4,5,7,8","1,2,7","1,2,4,7","1,2,4,7","2,4,7",null,"1,2,3,7",null,null,"2,7","1,2,7","1,2,3,4,7","1,2,3,4,7",null,null,"2,7,16","1",null,"1,2,4,7","1,2,7","1,2,3,4,7,8","1,2,7,8,17",null,null,"2","1,2,7","2,7","1,2,3,5,6,7"]],"container":"<table class=\"display\">\n  <thead>\n    <tr>\n      <th> <\/th>\n      <th>Cancer type<\/th>\n      <th>Cohort<\/th>\n      <th>Sequencing strategy<\/th>\n      <th>ID signature index<\/th>\n    <\/tr>\n  <\/thead>\n<\/table>","options":{"columnDefs":[{"orderable":false,"targets":0}],"order":[],"autoWidth":false,"orderClasses":false}},"evals":[],"jsHooks":[]}</script>
</div>
</div>
  <div class="chapter-nav">
<div class="prev"><a href="subtype-prediction.html"><span class="header-section-number">7</span> Subtype prediction</a></div>
<div class="next"><a href="datasets.html"><span class="header-section-number">9</span> Datasets</a></div>
</div></main><div class="col-md-3 col-lg-2 d-none d-md-block sidebar sidebar-chapter">
    <nav id="toc" data-toggle="toc" aria-label="On this page"><h2>On this page</h2>
      <ul class="nav navbar-nav">
<li><a class="nav-link" href="#sigflow"><span class="header-section-number">8</span> Sigflow pipeline</a></li>
<li><a class="nav-link" href="#cancer-type-specific-signature-index-database"><span class="header-section-number">8.1</span> Cancer type specific signature index database</a></li>
</ul>

      <div class="book-extra">
        <ul class="list-unstyled">
          
        </ul>
</div>
    </nav>
</div>

</div>
</div> <!-- .container -->

<footer class="bg-primary text-light mt-5"><div class="container"><div class="row">

  <div class="col-12 col-md-6 mt-3">
    <p>"<strong>Extract, Analyze and Visualize Mutational Signatures with Sigminer</strong>" was written by Shixiang Wang, PhD (Sun Yat-sen University Cancer Center), Xue-Song Liu, PhD (ShanghaiTech University). It was last built on 2022-08-29.</p>
  </div>

  <div class="col-12 col-md-6 mt-3">
    <p>This book was built by the <a class="text-light" href="https://bookdown.org">bookdown</a> R package.</p>
  </div>

</div></div>
</footer><!-- dynamically load mathjax for compatibility with self-contained --><script>
  (function () {
    var script = document.createElement("script");
    script.type = "text/javascript";
    var src = "true";
    if (src === "" || src === "true") src = "https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.9/latest.js?config=TeX-MML-AM_CHTML";
    if (location.protocol !== "file:")
      if (/^https?:/.test(src))
        src = src.replace(/^https?:/, '');
    script.src = src;
    document.getElementsByTagName("head")[0].appendChild(script);
  })();
</script><script type="text/x-mathjax-config">const popovers = document.querySelectorAll('a.footnote-ref[data-toggle="popover"]');
for (let popover of popovers) {
  const div = document.createElement('div');
  div.setAttribute('style', 'position: absolute; top: 0, left:0; width:0, height:0, overflow: hidden; visibility: hidden;');
  div.innerHTML = popover.getAttribute('data-content');

  var has_math = div.querySelector("span.math");
  if (has_math) {
    document.body.appendChild(div);
    MathJax.Hub.Queue(["Typeset", MathJax.Hub, div]);
    MathJax.Hub.Queue(function() {
      popover.setAttribute('data-content', div.innerHTML);
      document.body.removeChild(div);
    })
  }
}
</script>
</body>
</html>
